Stack leniency is covered by the rule that says "objects 1 beat apart or less must not fully overlap". When the stack leniency is low enough, objects no longer automatically stack and instead fully overlap. Note that mods like HR affect stack leniency, so mappers usually choose a stack leniency high enough that objects still stack with mods, or low enough that they stack nomod but not with mods.
The default stack leniency 7 is good for most maps, although there's nothing wrong with choosing a lower stack leniency for low diffs as long as you don't break the rule above. In this case you'd have to either manually stack objects or avoid mapping objects that would auto-stack otherwise.
Note that manually stacked objects will look "weird" compared to auto-stacked ones if the player plays the map with HR (since manually stacked objects are flipped), so avoid doing this on easier maps. Also note that
scaling BPM on the ranking criteria applies, so objects 1 beat apart can fully overlap at e.g. 90 BPM.